Starting phenix.real_space_refine on Tue Feb 20 13:51:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dju_7942/02_2024/6dju_7942_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dju_7942/02_2024/6dju_7942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dju_7942/02_2024/6dju_7942.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dju_7942/02_2024/6dju_7942.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dju_7942/02_2024/6dju_7942_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dju_7942/02_2024/6dju_7942_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 891 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 64 5.16 5 C 16875 2.51 5 N 4934 2.21 5 O 5233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 197": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 796": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 669": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D ARG 552": "NH1" <-> "NH2" Residue "D PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 669": "NH1" <-> "NH2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E ARG 552": "NH1" <-> "NH2" Residue "E ARG 588": "NH1" <-> "NH2" Residue "E PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 669": "NH1" <-> "NH2" Residue "E ARG 775": "NH1" <-> "NH2" Residue "E ARG 808": "NH1" <-> "NH2" Residue "F ARG 173": "NH1" <-> "NH2" Residue "F ARG 197": "NH1" <-> "NH2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F ARG 590": "NH1" <-> "NH2" Residue "F ARG 669": "NH1" <-> "NH2" Residue "F ARG 796": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27140 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4649 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 585} Chain breaks: 3 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4657 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 586} Chain breaks: 3 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4674 Classifications: {'peptide': 614} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 589} Chain breaks: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 4321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4321 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 24, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "N" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "E" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4230 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 23, 'TRANS': 524} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4115 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 21, 'TRANS': 509} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.10, per 1000 atoms: 0.52 Number of scatterers: 27140 At special positions: 0 Unit cell: (139.62, 147.138, 133.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 34 15.00 O 5233 8.00 N 4934 7.00 C 16875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.02 Conformation dependent library (CDL) restraints added in 5.0 seconds 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6428 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 165 helices and 23 sheets defined 41.7% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 301 through 304 No H-bonds generated for 'chain 'A' and resid 301 through 304' Processing helix chain 'A' and resid 317 through 323 removed outlier: 4.274A pdb=" N ARG A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 344 through 361 removed outlier: 3.737A pdb=" N ILE A 348 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 removed outlier: 4.261A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 406 removed outlier: 3.715A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 444 through 468 removed outlier: 3.565A pdb=" N LEU A 449 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 451 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 455 " --> pdb=" O GLN A 452 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 456 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 459 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 544 removed outlier: 3.510A pdb=" N ALA A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 removed outlier: 3.725A pdb=" N LEU A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG A 563 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLU A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASP A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 585 removed outlier: 3.656A pdb=" N ALA A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 590 No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 617 through 622 removed outlier: 4.517A pdb=" N ASP A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.631A pdb=" N ALA A 646 " --> pdb=" O HIS A 643 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A 647 " --> pdb=" O THR A 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 643 through 647' Processing helix chain 'A' and resid 665 through 668 No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 689 through 695 removed outlier: 5.415A pdb=" N GLN A 694 " --> pdb=" O ASP A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 741 through 746 removed outlier: 4.673A pdb=" N ARG A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 775 removed outlier: 3.651A pdb=" N VAL A 762 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG A 763 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP A 766 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 795 removed outlier: 3.680A pdb=" N ALA A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 795 " --> pdb=" O ARG A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 823 removed outlier: 3.527A pdb=" N ARG A 809 " --> pdb=" O ARG A 805 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLN A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 168 through 174 removed outlier: 4.295A pdb=" N GLU B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.576A pdb=" N SER B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.865A pdb=" N ALA B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 306' Processing helix chain 'B' and resid 317 through 323 removed outlier: 4.104A pdb=" N ARG B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.966A pdb=" N GLY B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 361 removed outlier: 3.730A pdb=" N GLU B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 355 through 361' Processing helix chain 'B' and resid 368 through 376 removed outlier: 3.633A pdb=" N VAL B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 406 removed outlier: 4.057A pdb=" N LEU B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 430 removed outlier: 3.552A pdb=" N VAL B 416 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 420 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 423 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 426 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 468 removed outlier: 3.565A pdb=" N LEU B 449 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP B 451 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 455 " --> pdb=" O GLN B 452 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 456 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 459 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 544 removed outlier: 3.871A pdb=" N ALA B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 576 through 578 No H-bonds generated for 'chain 'B' and resid 576 through 578' Processing helix chain 'B' and resid 582 through 585 No H-bonds generated for 'chain 'B' and resid 582 through 585' Processing helix chain 'B' and resid 587 through 591 Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 681 through 683 No H-bonds generated for 'chain 'B' and resid 681 through 683' Processing helix chain 'B' and resid 688 through 695 removed outlier: 4.462A pdb=" N GLN B 694 " --> pdb=" O ASP B 690 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 695 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 738 removed outlier: 3.604A pdb=" N ALA B 734 " --> pdb=" O GLN B 730 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 735 " --> pdb=" O VAL B 731 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 730 through 738' Processing helix chain 'B' and resid 741 through 744 No H-bonds generated for 'chain 'B' and resid 741 through 744' Processing helix chain 'B' and resid 759 through 777 removed outlier: 4.226A pdb=" N VAL B 762 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ARG B 763 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 764 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 777 " --> pdb=" O LYS B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 removed outlier: 4.204A pdb=" N ALA B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN B 795 " --> pdb=" O ARG B 791 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG B 796 " --> pdb=" O TRP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 823 removed outlier: 4.378A pdb=" N GLN B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY B 816 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASP B 817 " --> pdb=" O GLN B 813 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLN B 818 " --> pdb=" O ALA B 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 214 through 225 Processing helix chain 'C' and resid 254 through 268 removed outlier: 3.890A pdb=" N ARG C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 300 through 304 removed outlier: 3.762A pdb=" N LEU C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 4.055A pdb=" N ALA C 328 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA C 329 " --> pdb=" O LYS C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 353 removed outlier: 4.674A pdb=" N GLY C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C 353 " --> pdb=" O GLY C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 368 through 379 removed outlier: 3.701A pdb=" N THR C 376 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 406 removed outlier: 4.328A pdb=" N ASP C 393 " --> pdb=" O ASP C 389 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU C 394 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 430 Processing helix chain 'C' and resid 444 through 468 removed outlier: 3.566A pdb=" N LEU C 449 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP C 451 " --> pdb=" O GLU C 448 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 455 " --> pdb=" O GLN C 452 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 456 " --> pdb=" O LYS C 453 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 459 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 558 through 562 Processing helix chain 'C' and resid 564 through 570 removed outlier: 4.033A pdb=" N LYS C 570 " --> pdb=" O ASP C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 578 No H-bonds generated for 'chain 'C' and resid 576 through 578' Processing helix chain 'C' and resid 580 through 587 removed outlier: 3.864A pdb=" N ALA C 585 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 586 " --> pdb=" O VAL C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 624 removed outlier: 3.941A pdb=" N ALA C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA C 621 " --> pdb=" O ALA C 617 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP C 622 " --> pdb=" O LYS C 618 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE C 623 " --> pdb=" O ALA C 619 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 648 removed outlier: 3.885A pdb=" N ALA C 646 " --> pdb=" O HIS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 738 removed outlier: 3.956A pdb=" N ARG C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 778 removed outlier: 3.660A pdb=" N LEU C 776 " --> pdb=" O LEU C 772 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA C 777 " --> pdb=" O GLY C 773 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLN C 778 " --> pdb=" O LYS C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 795 removed outlier: 3.859A pdb=" N ALA C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 814 removed outlier: 3.939A pdb=" N ARG C 809 " --> pdb=" O ARG C 805 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C 812 " --> pdb=" O ARG C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.935A pdb=" N GLU D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 194 removed outlier: 3.513A pdb=" N ARG D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 193 " --> pdb=" O ARG D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 225 Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.518A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.876A pdb=" N ALA D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG D 306 " --> pdb=" O PRO D 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 301 through 306' Processing helix chain 'D' and resid 317 through 323 removed outlier: 3.854A pdb=" N ARG D 321 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 353 Processing helix chain 'D' and resid 355 through 361 removed outlier: 3.911A pdb=" N GLU D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 360 " --> pdb=" O ASP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 377 Processing helix chain 'D' and resid 387 through 406 removed outlier: 3.542A pdb=" N ALA D 391 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU D 394 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 544 Processing helix chain 'D' and resid 557 through 562 Processing helix chain 'D' and resid 568 through 570 No H-bonds generated for 'chain 'D' and resid 568 through 570' Processing helix chain 'D' and resid 580 through 591 removed outlier: 4.061A pdb=" N ARG D 588 " --> pdb=" O ASP D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 623 Processing helix chain 'D' and resid 643 through 647 removed outlier: 3.769A pdb=" N ALA D 646 " --> pdb=" O HIS D 643 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 643 through 647' Processing helix chain 'D' and resid 663 through 669 removed outlier: 3.970A pdb=" N VAL D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 695 removed outlier: 4.194A pdb=" N GLN D 694 " --> pdb=" O ASP D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 738 removed outlier: 3.556A pdb=" N ARG D 736 " --> pdb=" O LEU D 732 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA D 737 " --> pdb=" O ALA D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 744 No H-bonds generated for 'chain 'D' and resid 741 through 744' Processing helix chain 'D' and resid 760 through 775 removed outlier: 3.877A pdb=" N ILE D 764 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 795 Processing helix chain 'D' and resid 803 through 806 Proline residue: D 806 - end of helix No H-bonds generated for 'chain 'D' and resid 803 through 806' Processing helix chain 'D' and resid 808 through 820 removed outlier: 4.458A pdb=" N ASP D 817 " --> pdb=" O GLN D 813 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLN D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.920A pdb=" N ARG E 173 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU E 174 " --> pdb=" O ARG E 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 170 through 174' Processing helix chain 'E' and resid 186 through 193 Processing helix chain 'E' and resid 212 through 225 Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 255 through 269 removed outlier: 3.802A pdb=" N ASP E 264 " --> pdb=" O LYS E 260 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE E 266 " --> pdb=" O VAL E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.488A pdb=" N ARG E 306 " --> pdb=" O PRO E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 No H-bonds generated for 'chain 'E' and resid 317 through 320' Processing helix chain 'E' and resid 331 through 333 No H-bonds generated for 'chain 'E' and resid 331 through 333' Processing helix chain 'E' and resid 344 through 353 removed outlier: 3.647A pdb=" N GLY E 349 " --> pdb=" O GLU E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 361 removed outlier: 4.061A pdb=" N HIS E 361 " --> pdb=" O ARG E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 381 removed outlier: 3.934A pdb=" N ARG E 380 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR E 381 " --> pdb=" O LEU E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 405 removed outlier: 3.607A pdb=" N ALA E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU E 394 " --> pdb=" O LYS E 390 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU E 405 " --> pdb=" O ARG E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 546 removed outlier: 3.988A pdb=" N ASP E 540 " --> pdb=" O ASP E 536 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL E 542 " --> pdb=" O ILE E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 562 Processing helix chain 'E' and resid 568 through 570 No H-bonds generated for 'chain 'E' and resid 568 through 570' Processing helix chain 'E' and resid 576 through 591 removed outlier: 3.842A pdb=" N SER E 589 " --> pdb=" O ALA E 585 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG E 590 " --> pdb=" O VAL E 586 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA E 591 " --> pdb=" O ARG E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 621 Processing helix chain 'E' and resid 646 through 648 No H-bonds generated for 'chain 'E' and resid 646 through 648' Processing helix chain 'E' and resid 665 through 667 No H-bonds generated for 'chain 'E' and resid 665 through 667' Processing helix chain 'E' and resid 681 through 683 No H-bonds generated for 'chain 'E' and resid 681 through 683' Processing helix chain 'E' and resid 689 through 695 removed outlier: 3.750A pdb=" N VAL E 695 " --> pdb=" O VAL E 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 730 through 738 Processing helix chain 'E' and resid 741 through 746 removed outlier: 3.569A pdb=" N ILE E 744 " --> pdb=" O PRO E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 759 through 771 removed outlier: 3.750A pdb=" N VAL E 762 " --> pdb=" O GLU E 759 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ARG E 763 " --> pdb=" O GLU E 760 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE E 764 " --> pdb=" O LEU E 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 797 removed outlier: 4.085A pdb=" N TRP E 792 " --> pdb=" O PRO E 788 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU E 793 " --> pdb=" O ALA E 789 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ALA E 794 " --> pdb=" O LYS E 790 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN E 795 " --> pdb=" O ARG E 791 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG E 796 " --> pdb=" O TRP E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 825 removed outlier: 3.920A pdb=" N VAL E 811 " --> pdb=" O LEU E 807 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN E 812 " --> pdb=" O ARG E 808 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA E 814 " --> pdb=" O LEU E 810 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS E 821 " --> pdb=" O ASP E 817 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET E 822 " --> pdb=" O GLN E 818 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU E 824 " --> pdb=" O ALA E 820 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 174 Processing helix chain 'F' and resid 184 through 194 Processing helix chain 'F' and resid 212 through 225 Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 259 through 262 No H-bonds generated for 'chain 'F' and resid 259 through 262' Processing helix chain 'F' and resid 264 through 267 No H-bonds generated for 'chain 'F' and resid 264 through 267' Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 301 through 304 No H-bonds generated for 'chain 'F' and resid 301 through 304' Processing helix chain 'F' and resid 317 through 322 Processing helix chain 'F' and resid 344 through 349 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 368 through 374 Processing helix chain 'F' and resid 388 through 405 removed outlier: 3.880A pdb=" N ILE F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 542 Processing helix chain 'F' and resid 557 through 560 No H-bonds generated for 'chain 'F' and resid 557 through 560' Processing helix chain 'F' and resid 568 through 571 No H-bonds generated for 'chain 'F' and resid 568 through 571' Processing helix chain 'F' and resid 576 through 589 Processing helix chain 'F' and resid 613 through 624 removed outlier: 3.801A pdb=" N ALA F 617 " --> pdb=" O LYS F 613 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU F 620 " --> pdb=" O LEU F 616 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA F 621 " --> pdb=" O ALA F 617 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP F 622 " --> pdb=" O LYS F 618 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE F 623 " --> pdb=" O ALA F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 636 through 638 No H-bonds generated for 'chain 'F' and resid 636 through 638' Processing helix chain 'F' and resid 644 through 647 removed outlier: 3.801A pdb=" N ARG F 647 " --> pdb=" O THR F 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 644 through 647' Processing helix chain 'F' and resid 664 through 670 Processing helix chain 'F' and resid 686 through 695 removed outlier: 3.962A pdb=" N ASP F 690 " --> pdb=" O PRO F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 738 removed outlier: 3.600A pdb=" N THR F 738 " --> pdb=" O ALA F 734 " (cutoff:3.500A) Processing helix chain 'F' and resid 759 through 776 removed outlier: 4.213A pdb=" N VAL F 762 " --> pdb=" O GLU F 759 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ARG F 763 " --> pdb=" O GLU F 760 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE F 764 " --> pdb=" O LEU F 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 792 Processing helix chain 'F' and resid 795 through 797 No H-bonds generated for 'chain 'F' and resid 795 through 797' Processing helix chain 'F' and resid 805 through 824 removed outlier: 3.880A pdb=" N GLN F 812 " --> pdb=" O ARG F 808 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE F 815 " --> pdb=" O VAL F 811 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN F 818 " --> pdb=" O ALA F 814 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU F 824 " --> pdb=" O ALA F 820 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 335 through 338 removed outlier: 7.062A pdb=" N GLY A 313 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA A 314 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 601 through 605 removed outlier: 3.611A pdb=" N LEU A 718 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL A 632 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N ASP A 679 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE A 634 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 700 through 702 Processing sheet with id= D, first strand: chain 'A' and resid 783 through 785 removed outlier: 6.999A pdb=" N VAL A 834 " --> pdb=" O GLN A 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 335 through 338 removed outlier: 6.417A pdb=" N GLY B 313 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N GLY B 206 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR B 315 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 236 through 239 removed outlier: 6.123A pdb=" N ARG B 310 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 601 through 605 removed outlier: 3.714A pdb=" N PHE B 603 " --> pdb=" O LEU B 716 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 632 through 635 removed outlier: 4.213A pdb=" N ILE B 634 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP B 679 " --> pdb=" O ILE B 634 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 782 through 785 Processing sheet with id= J, first strand: chain 'C' and resid 335 through 338 removed outlier: 6.707A pdb=" N GLY C 313 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N GLY C 206 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR C 315 " --> pdb=" O GLY C 206 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA C 314 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 601 through 604 removed outlier: 3.929A pdb=" N PHE C 603 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 718 " --> pdb=" O PHE C 603 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 632 through 635 removed outlier: 3.843A pdb=" N ILE C 634 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 700 through 702 Processing sheet with id= N, first strand: chain 'C' and resid 837 through 839 Processing sheet with id= O, first strand: chain 'D' and resid 202 through 206 removed outlier: 6.435A pdb=" N GLN D 335 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE D 205 " --> pdb=" O GLN D 335 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL D 337 " --> pdb=" O ILE D 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 276 through 278 removed outlier: 6.104A pdb=" N VAL D 312 " --> pdb=" O ILE D 277 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 632 through 635 removed outlier: 3.678A pdb=" N ILE D 634 " --> pdb=" O LEU D 677 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP D 679 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE D 715 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE D 678 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE D 717 " --> pdb=" O PHE D 678 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 700 through 702 removed outlier: 3.634A pdb=" N LEU D 701 " --> pdb=" O VAL D 709 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 313 through 315 Processing sheet with id= T, first strand: chain 'E' and resid 631 through 635 removed outlier: 5.824A pdb=" N VAL E 675 " --> pdb=" O VAL E 632 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE E 634 " --> pdb=" O VAL E 675 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU E 677 " --> pdb=" O ILE E 634 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE E 715 " --> pdb=" O VAL E 676 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N PHE E 678 " --> pdb=" O ILE E 715 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE E 717 " --> pdb=" O PHE E 678 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 203 through 205 Processing sheet with id= V, first strand: chain 'F' and resid 601 through 606 removed outlier: 7.052A pdb=" N VAL F 676 " --> pdb=" O ILE F 717 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N THR F 719 " --> pdb=" O VAL F 676 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N PHE F 678 " --> pdb=" O THR F 719 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 782 through 784 696 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.56 Time building geometry restraints manager: 10.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 10327 1.38 - 1.55: 17008 1.55 - 1.73: 56 1.73 - 1.90: 108 1.90 - 2.08: 10 Bond restraints: 27509 Sorted by residual: bond pdb=" C4 AGS D 902 " pdb=" C5 AGS D 902 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.20e+01 bond pdb=" C5 AGS D 902 " pdb=" C6 AGS D 902 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.38e+01 bond pdb=" PG AGS D 902 " pdb=" S1G AGS D 902 " ideal model delta sigma weight residual 1.949 2.075 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" CB THR C 460 " pdb=" OG1 THR C 460 " ideal model delta sigma weight residual 1.433 1.532 -0.099 1.60e-02 3.91e+03 3.81e+01 bond pdb=" CB THR A 460 " pdb=" OG1 THR A 460 " ideal model delta sigma weight residual 1.433 1.531 -0.098 1.60e-02 3.91e+03 3.73e+01 ... (remaining 27504 not shown) Histogram of bond angle deviations from ideal: 90.44 - 99.88: 15 99.88 - 109.31: 2924 109.31 - 118.75: 19442 118.75 - 128.18: 14650 128.18 - 137.62: 193 Bond angle restraints: 37224 Sorted by residual: angle pdb=" N GLY D 574 " pdb=" CA GLY D 574 " pdb=" C GLY D 574 " ideal model delta sigma weight residual 110.56 90.44 20.12 1.36e+00 5.41e-01 2.19e+02 angle pdb=" C ILE D 573 " pdb=" CA ILE D 573 " pdb=" CB ILE D 573 " ideal model delta sigma weight residual 111.29 92.71 18.58 1.64e+00 3.72e-01 1.28e+02 angle pdb=" C5 AGS D 902 " pdb=" C4 AGS D 902 " pdb=" N3 AGS D 902 " ideal model delta sigma weight residual 126.80 118.71 8.09 7.41e-01 1.82e+00 1.19e+02 angle pdb=" C4 AGS D 902 " pdb=" C5 AGS D 902 " pdb=" N7 AGS D 902 " ideal model delta sigma weight residual 110.73 106.59 4.14 4.52e-01 4.89e+00 8.41e+01 angle pdb=" C5 AGS D 902 " pdb=" N7 AGS D 902 " pdb=" C8 AGS D 902 " ideal model delta sigma weight residual 103.67 107.48 -3.81 4.26e-01 5.51e+00 7.99e+01 ... (remaining 37219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.43: 16500 31.43 - 62.86: 420 62.86 - 94.29: 24 94.29 - 125.72: 3 125.72 - 157.15: 5 Dihedral angle restraints: 16952 sinusoidal: 6985 harmonic: 9967 Sorted by residual: dihedral pdb=" CA LEU B 387 " pdb=" C LEU B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta harmonic sigma weight residual 180.00 -118.14 -61.86 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA LEU F 553 " pdb=" C LEU F 553 " pdb=" N LEU F 554 " pdb=" CA LEU F 554 " ideal model delta harmonic sigma weight residual -180.00 -118.71 -61.29 0 5.00e+00 4.00e-02 1.50e+02 dihedral pdb=" CA SER D 839 " pdb=" C SER D 839 " pdb=" N PRO D 840 " pdb=" CA PRO D 840 " ideal model delta harmonic sigma weight residual -180.00 -125.19 -54.81 0 5.00e+00 4.00e-02 1.20e+02 ... (remaining 16949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3657 0.084 - 0.169: 574 0.169 - 0.253: 38 0.253 - 0.337: 9 0.337 - 0.421: 2 Chirality restraints: 4280 Sorted by residual: chirality pdb=" CB ILE F 324 " pdb=" CA ILE F 324 " pdb=" CG1 ILE F 324 " pdb=" CG2 ILE F 324 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CB ILE D 681 " pdb=" CA ILE D 681 " pdb=" CG1 ILE D 681 " pdb=" CG2 ILE D 681 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA PRO B 388 " pdb=" N PRO B 388 " pdb=" C PRO B 388 " pdb=" CB PRO B 388 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 4277 not shown) Planarity restraints: 4856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 409 " -0.080 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO C 410 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO C 410 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 410 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 554 " 0.024 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C LEU F 554 " -0.084 2.00e-02 2.50e+03 pdb=" O LEU F 554 " 0.032 2.00e-02 2.50e+03 pdb=" N GLU F 555 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 740 " 0.073 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO F 741 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO F 741 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO F 741 " 0.062 5.00e-02 4.00e+02 ... (remaining 4853 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 165 2.55 - 3.14: 20483 3.14 - 3.72: 39583 3.72 - 4.31: 51984 4.31 - 4.90: 85462 Nonbonded interactions: 197677 Sorted by model distance: nonbonded pdb=" O ILE D 573 " pdb=" CG2 ILE D 573 " model vdw 1.960 3.460 nonbonded pdb=" O GLU A 412 " pdb=" N GLU A 415 " model vdw 2.093 2.520 nonbonded pdb=" O GLU B 412 " pdb=" N ASP B 414 " model vdw 2.168 2.520 nonbonded pdb=" CD2 LEU B 430 " pdb=" OD2 ASP C 368 " model vdw 2.194 3.460 nonbonded pdb=" N GLY D 574 " pdb=" O GLY D 574 " model vdw 2.216 2.496 ... (remaining 197672 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 650 or resid 663 through 845 or resid 901)) selection = (chain 'B' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 650 or resid 663 through 845 or resid 901)) selection = (chain 'C' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 650 or resid 663 through 845 or resid 901)) selection = (chain 'D' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 650 or resid 663 through 845 or resid 901)) selection = (chain 'E' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 650 or resid 663 through 845 or resid 901)) selection = (chain 'F' and (resid 159 through 845 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 7.110 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 67.460 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.135 27509 Z= 0.478 Angle : 1.149 20.120 37224 Z= 0.632 Chirality : 0.060 0.421 4280 Planarity : 0.008 0.123 4856 Dihedral : 13.625 157.148 10524 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.04 % Favored : 86.41 % Rotamer: Outliers : 0.90 % Allowed : 6.73 % Favored : 92.37 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.29 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.12 (0.11), residues: 3452 helix: -3.44 (0.09), residues: 1484 sheet: -3.14 (0.25), residues: 299 loop : -3.39 (0.13), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 545 HIS 0.007 0.002 HIS C 643 PHE 0.032 0.004 PHE B 753 TYR 0.029 0.003 TYR C 381 ARG 0.012 0.001 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 671 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.8701 (mmm) cc_final: 0.8495 (mmm) REVERT: A 277 ILE cc_start: 0.9276 (mt) cc_final: 0.9066 (tp) REVERT: A 330 LEU cc_start: 0.7680 (mt) cc_final: 0.7420 (mt) REVERT: A 584 ASP cc_start: 0.6326 (t0) cc_final: 0.5707 (t0) REVERT: B 186 GLU cc_start: 0.7239 (mp0) cc_final: 0.7003 (mp0) REVERT: B 331 GLU cc_start: 0.8204 (pp20) cc_final: 0.7980 (pp20) REVERT: B 396 ASP cc_start: 0.7681 (t0) cc_final: 0.7480 (t0) REVERT: C 265 ASP cc_start: 0.7940 (t0) cc_final: 0.7730 (t0) REVERT: C 277 ILE cc_start: 0.9306 (mt) cc_final: 0.9102 (tt) REVERT: C 332 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8043 (ppp-140) REVERT: C 335 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7679 (mm-40) REVERT: C 383 THR cc_start: 0.8704 (m) cc_final: 0.8445 (t) REVERT: C 400 SER cc_start: 0.9344 (m) cc_final: 0.9048 (t) REVERT: C 442 LEU cc_start: 0.5403 (OUTLIER) cc_final: 0.5175 (pt) REVERT: C 554 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7132 (tp) REVERT: C 709 VAL cc_start: 0.9387 (p) cc_final: 0.9034 (m) REVERT: D 277 ILE cc_start: 0.9311 (mt) cc_final: 0.8984 (tt) REVERT: D 635 ASP cc_start: 0.8717 (t0) cc_final: 0.8396 (t70) REVERT: D 697 ASP cc_start: 0.7219 (t70) cc_final: 0.6998 (t0) REVERT: D 698 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8398 (mm-30) REVERT: E 278 ASP cc_start: 0.7834 (t70) cc_final: 0.7131 (p0) REVERT: E 306 ARG cc_start: 0.8261 (ttm170) cc_final: 0.7994 (ttm170) REVERT: E 319 GLU cc_start: 0.8136 (mp0) cc_final: 0.7890 (mp0) REVERT: E 615 GLU cc_start: 0.7936 (tp30) cc_final: 0.7702 (tp30) REVERT: E 687 ASP cc_start: 0.7554 (t0) cc_final: 0.6916 (t0) REVERT: E 783 LEU cc_start: 0.7509 (mp) cc_final: 0.6945 (tt) REVERT: F 194 LEU cc_start: 0.9193 (tm) cc_final: 0.8637 (mt) REVERT: F 299 MET cc_start: 0.8255 (tpt) cc_final: 0.7956 (tpt) REVERT: F 336 GLN cc_start: 0.8036 (pm20) cc_final: 0.7638 (pp30) REVERT: F 571 ARG cc_start: 0.8277 (tpp80) cc_final: 0.7929 (tpp80) REVERT: F 615 GLU cc_start: 0.7629 (tp30) cc_final: 0.6907 (tp30) REVERT: F 669 ARG cc_start: 0.7916 (ttt180) cc_final: 0.6957 (ttm110) outliers start: 25 outliers final: 10 residues processed: 695 average time/residue: 0.4850 time to fit residues: 485.5120 Evaluate side-chains 336 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 323 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 409 ARG Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 554 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 8.9990 chunk 263 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 90 optimal weight: 0.0980 chunk 177 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 272 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 203 optimal weight: 9.9990 chunk 316 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 643 HIS A 705 HIS B 643 HIS B 663 GLN C 336 GLN C 705 HIS C 813 GLN D 335 GLN D 336 GLN D 361 HIS E 335 GLN E 336 GLN E 575 GLN E 827 GLN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 784 GLN F 795 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27509 Z= 0.225 Angle : 0.725 10.477 37224 Z= 0.367 Chirality : 0.045 0.286 4280 Planarity : 0.006 0.089 4856 Dihedral : 11.806 148.001 4091 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.56 % Favored : 88.09 % Rotamer: Outliers : 3.78 % Allowed : 13.58 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.13), residues: 3452 helix: -2.16 (0.11), residues: 1501 sheet: -2.83 (0.27), residues: 272 loop : -3.02 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 545 HIS 0.008 0.001 HIS A 281 PHE 0.020 0.002 PHE F 739 TYR 0.017 0.002 TYR D 251 ARG 0.008 0.001 ARG A 670 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 377 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8209 (tpp) cc_final: 0.7842 (tpp) REVERT: A 631 MET cc_start: 0.8004 (ttp) cc_final: 0.7661 (ttt) REVERT: B 186 GLU cc_start: 0.7277 (mp0) cc_final: 0.6982 (mp0) REVERT: B 327 ASP cc_start: 0.8051 (t0) cc_final: 0.7686 (t0) REVERT: B 331 GLU cc_start: 0.8460 (pp20) cc_final: 0.8111 (pp20) REVERT: B 637 SER cc_start: 0.8850 (p) cc_final: 0.8642 (p) REVERT: B 703 ASP cc_start: 0.9105 (p0) cc_final: 0.8790 (p0) REVERT: C 199 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7972 (ttpp) REVERT: C 257 GLU cc_start: 0.8479 (pm20) cc_final: 0.8265 (pm20) REVERT: C 265 ASP cc_start: 0.8023 (t0) cc_final: 0.7676 (t70) REVERT: C 400 SER cc_start: 0.9290 (m) cc_final: 0.9002 (t) REVERT: C 442 LEU cc_start: 0.5590 (OUTLIER) cc_final: 0.5008 (pt) REVERT: C 554 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7351 (tp) REVERT: D 254 GLU cc_start: 0.8074 (tp30) cc_final: 0.7791 (tp30) REVERT: D 325 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7449 (tm-30) REVERT: D 648 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8601 (pp) REVERT: D 670 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7163 (ptt-90) REVERT: D 710 ASP cc_start: 0.8335 (p0) cc_final: 0.7791 (p0) REVERT: E 306 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7938 (ttm170) REVERT: E 319 GLU cc_start: 0.8234 (mp0) cc_final: 0.7915 (mp0) REVERT: E 388 PRO cc_start: 0.8529 (Cg_exo) cc_final: 0.8288 (Cg_endo) REVERT: E 604 MET cc_start: 0.7851 (ppp) cc_final: 0.7485 (ppp) REVERT: E 615 GLU cc_start: 0.8024 (tp30) cc_final: 0.7571 (tp30) REVERT: E 687 ASP cc_start: 0.7626 (t0) cc_final: 0.7059 (t0) REVERT: E 783 LEU cc_start: 0.7635 (mp) cc_final: 0.7009 (tt) REVERT: E 822 MET cc_start: 0.6992 (tpp) cc_final: 0.6636 (mpp) REVERT: F 215 ILE cc_start: 0.9266 (mt) cc_final: 0.9050 (mm) REVERT: F 336 GLN cc_start: 0.8062 (pm20) cc_final: 0.7669 (pp30) REVERT: F 669 ARG cc_start: 0.8210 (ttt180) cc_final: 0.7100 (ptp-110) REVERT: F 739 PHE cc_start: 0.7230 (m-80) cc_final: 0.6695 (m-10) REVERT: F 822 MET cc_start: 0.7696 (mmt) cc_final: 0.7486 (mmm) REVERT: F 845 LEU cc_start: 0.7226 (mt) cc_final: 0.6999 (mt) outliers start: 105 outliers final: 48 residues processed: 452 average time/residue: 0.4198 time to fit residues: 290.9927 Evaluate side-chains 334 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 281 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 670 ARG Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 774 LYS Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 710 ASP Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 829 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 316 optimal weight: 5.9990 chunk 342 optimal weight: 9.9990 chunk 281 optimal weight: 0.1980 chunk 313 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 253 optimal weight: 7.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 HIS A 575 GLN C 685 HIS E 201 ASN E 778 GLN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 784 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27509 Z= 0.294 Angle : 0.735 15.094 37224 Z= 0.364 Chirality : 0.046 0.264 4280 Planarity : 0.006 0.090 4856 Dihedral : 11.517 155.393 4073 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.46 % Favored : 87.20 % Rotamer: Outliers : 4.61 % Allowed : 15.02 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.13), residues: 3452 helix: -1.54 (0.12), residues: 1499 sheet: -2.76 (0.25), residues: 292 loop : -2.87 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 545 HIS 0.009 0.001 HIS E 361 PHE 0.024 0.002 PHE A 605 TYR 0.016 0.002 TYR F 320 ARG 0.006 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 284 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ARG cc_start: 0.7978 (tpt170) cc_final: 0.7453 (mmm-85) REVERT: B 327 ASP cc_start: 0.8048 (t0) cc_final: 0.7654 (t0) REVERT: B 331 GLU cc_start: 0.8586 (pp20) cc_final: 0.8242 (pp20) REVERT: B 387 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7198 (mm) REVERT: B 442 LEU cc_start: 0.5050 (OUTLIER) cc_final: 0.4451 (tt) REVERT: C 199 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8019 (ttpp) REVERT: C 265 ASP cc_start: 0.8042 (t0) cc_final: 0.7758 (t70) REVERT: C 442 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.4830 (pt) REVERT: D 325 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7503 (tm-30) REVERT: D 670 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7166 (ptt-90) REVERT: D 798 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: E 319 GLU cc_start: 0.8369 (mp0) cc_final: 0.7929 (mp0) REVERT: E 604 MET cc_start: 0.7999 (ppp) cc_final: 0.7795 (ppp) REVERT: E 615 GLU cc_start: 0.8096 (tp30) cc_final: 0.7618 (tp30) REVERT: E 687 ASP cc_start: 0.7652 (t0) cc_final: 0.7136 (t0) REVERT: E 783 LEU cc_start: 0.7621 (mp) cc_final: 0.6994 (tt) REVERT: E 822 MET cc_start: 0.6979 (tpp) cc_final: 0.6560 (tpp) REVERT: F 194 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8744 (mt) REVERT: F 330 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6729 (pp) REVERT: F 336 GLN cc_start: 0.8026 (pm20) cc_final: 0.7667 (pp30) REVERT: F 669 ARG cc_start: 0.8241 (ttt180) cc_final: 0.7110 (ptp-110) REVERT: F 739 PHE cc_start: 0.7235 (m-80) cc_final: 0.6700 (m-10) outliers start: 128 outliers final: 67 residues processed: 374 average time/residue: 0.3831 time to fit residues: 227.7268 Evaluate side-chains 322 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 247 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 761 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 670 ARG Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 774 LYS Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 798 PHE Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 697 ASP Chi-restraints excluded: chain E residue 710 ASP Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 564 MET Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 829 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 0.1980 chunk 238 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 317 optimal weight: 40.0000 chunk 336 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 overall best weight: 4.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS C 643 HIS E 201 ASN E 771 GLN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 784 GLN F 818 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 27509 Z= 0.425 Angle : 0.805 12.064 37224 Z= 0.397 Chirality : 0.049 0.272 4280 Planarity : 0.006 0.093 4856 Dihedral : 11.459 157.760 4071 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.44 % Favored : 86.27 % Rotamer: Outliers : 5.83 % Allowed : 15.88 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.13), residues: 3452 helix: -1.38 (0.13), residues: 1511 sheet: -2.76 (0.25), residues: 295 loop : -2.95 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 545 HIS 0.006 0.002 HIS E 361 PHE 0.031 0.003 PHE A 605 TYR 0.018 0.002 TYR C 655 ARG 0.008 0.001 ARG D 796 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 257 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8767 (tt) REVERT: A 843 ASP cc_start: 0.9008 (OUTLIER) cc_final: 0.8599 (p0) REVERT: B 201 ASN cc_start: 0.9536 (OUTLIER) cc_final: 0.9311 (p0) REVERT: B 319 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7164 (mm-30) REVERT: B 327 ASP cc_start: 0.8156 (t0) cc_final: 0.7871 (t0) REVERT: B 331 GLU cc_start: 0.8772 (pp20) cc_final: 0.8403 (pp20) REVERT: B 442 LEU cc_start: 0.4662 (OUTLIER) cc_final: 0.3969 (tt) REVERT: B 663 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7142 (mm-40) REVERT: C 265 ASP cc_start: 0.8129 (t0) cc_final: 0.7886 (t0) REVERT: C 713 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8537 (p0) REVERT: C 818 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8515 (mt0) REVERT: C 827 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7105 (pt0) REVERT: C 828 VAL cc_start: 0.8437 (OUTLIER) cc_final: 0.8225 (t) REVERT: D 254 GLU cc_start: 0.8392 (tp30) cc_final: 0.8174 (tp30) REVERT: D 670 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7360 (ptt-90) REVERT: D 798 PHE cc_start: 0.8684 (m-80) cc_final: 0.8424 (m-80) REVERT: E 318 ASP cc_start: 0.7564 (p0) cc_final: 0.7265 (p0) REVERT: E 615 GLU cc_start: 0.8179 (tp30) cc_final: 0.7621 (tp30) REVERT: E 687 ASP cc_start: 0.7621 (t0) cc_final: 0.7167 (t0) REVERT: E 783 LEU cc_start: 0.7690 (mp) cc_final: 0.7013 (tt) REVERT: E 822 MET cc_start: 0.6953 (tpp) cc_final: 0.6556 (tpp) REVERT: F 187 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6186 (mp) REVERT: F 194 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8801 (mt) REVERT: F 330 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6679 (pp) REVERT: F 336 GLN cc_start: 0.8118 (pm20) cc_final: 0.7627 (pp30) REVERT: F 669 ARG cc_start: 0.8180 (ttt180) cc_final: 0.7045 (ptp-110) REVERT: F 739 PHE cc_start: 0.7275 (m-80) cc_final: 0.6726 (m-10) outliers start: 162 outliers final: 99 residues processed: 380 average time/residue: 0.3682 time to fit residues: 223.3905 Evaluate side-chains 334 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 221 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 829 HIS Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 620 LEU Chi-restraints excluded: chain B residue 626 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 663 GLN Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 584 ASP Chi-restraints excluded: chain C residue 635 ASP Chi-restraints excluded: chain C residue 644 THR Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 818 GLN Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 670 ARG Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 774 LYS Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 636 MET Chi-restraints excluded: chain E residue 693 LEU Chi-restraints excluded: chain E residue 697 ASP Chi-restraints excluded: chain E residue 710 ASP Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 564 MET Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 721 ASN Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 743 PHE Chi-restraints excluded: chain F residue 776 LEU Chi-restraints excluded: chain F residue 784 GLN Chi-restraints excluded: chain F residue 793 LEU Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 829 HIS Chi-restraints excluded: chain F residue 843 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 250 optimal weight: 20.0000 chunk 138 optimal weight: 0.6980 chunk 287 optimal weight: 0.5980 chunk 232 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 0.0980 chunk 301 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 HIS C 597 ASN ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 27509 Z= 0.163 Angle : 0.667 12.411 37224 Z= 0.326 Chirality : 0.044 0.274 4280 Planarity : 0.005 0.087 4856 Dihedral : 10.742 160.422 4069 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.92 % Favored : 88.88 % Rotamer: Outliers : 3.82 % Allowed : 18.40 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.14), residues: 3452 helix: -1.01 (0.13), residues: 1497 sheet: -2.35 (0.26), residues: 295 loop : -2.73 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 792 HIS 0.004 0.001 HIS E 361 PHE 0.018 0.001 PHE D 386 TYR 0.018 0.001 TYR F 338 ARG 0.008 0.000 ARG F 671 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 279 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: B 201 ASN cc_start: 0.9472 (OUTLIER) cc_final: 0.9235 (p0) REVERT: B 319 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6891 (mm-30) REVERT: B 327 ASP cc_start: 0.8074 (t0) cc_final: 0.7604 (t0) REVERT: B 331 GLU cc_start: 0.8753 (pp20) cc_final: 0.8490 (pp20) REVERT: B 387 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7170 (mm) REVERT: B 442 LEU cc_start: 0.4836 (OUTLIER) cc_final: 0.4004 (tt) REVERT: B 663 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7020 (mm-40) REVERT: B 692 LEU cc_start: 0.9431 (tp) cc_final: 0.9208 (tt) REVERT: C 234 ASP cc_start: 0.8170 (m-30) cc_final: 0.7892 (t0) REVERT: C 265 ASP cc_start: 0.8025 (t0) cc_final: 0.7719 (t70) REVERT: C 818 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8500 (mt0) REVERT: D 254 GLU cc_start: 0.8221 (tp30) cc_final: 0.7983 (tp30) REVERT: D 259 LEU cc_start: 0.9304 (tp) cc_final: 0.9056 (tp) REVERT: D 798 PHE cc_start: 0.8669 (m-80) cc_final: 0.8444 (m-80) REVERT: E 615 GLU cc_start: 0.8007 (tp30) cc_final: 0.7641 (tp30) REVERT: E 687 ASP cc_start: 0.7546 (t0) cc_final: 0.7184 (t0) REVERT: E 697 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: E 783 LEU cc_start: 0.7593 (mp) cc_final: 0.6966 (tt) REVERT: E 822 MET cc_start: 0.7034 (tpp) cc_final: 0.6656 (tpp) REVERT: F 330 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6589 (pp) REVERT: F 336 GLN cc_start: 0.8094 (pm20) cc_final: 0.7668 (pp30) REVERT: F 590 ARG cc_start: 0.6979 (tpt-90) cc_final: 0.6689 (tpt-90) REVERT: F 596 PRO cc_start: 0.6067 (Cg_endo) cc_final: 0.5446 (Cg_exo) REVERT: F 669 ARG cc_start: 0.8137 (ttt180) cc_final: 0.6759 (mtm110) REVERT: F 739 PHE cc_start: 0.7114 (m-80) cc_final: 0.6562 (m-10) REVERT: F 812 GLN cc_start: 0.8878 (tp-100) cc_final: 0.8671 (tp-100) outliers start: 106 outliers final: 61 residues processed: 354 average time/residue: 0.3694 time to fit residues: 210.1662 Evaluate side-chains 319 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 249 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 829 HIS Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 663 GLN Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 818 GLN Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 774 LYS Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 697 ASP Chi-restraints excluded: chain E residue 710 ASP Chi-restraints excluded: chain E residue 732 LEU Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 843 ASP Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 564 MET Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 793 LEU Chi-restraints excluded: chain F residue 829 HIS Chi-restraints excluded: chain F residue 843 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 0.9990 chunk 302 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 336 optimal weight: 9.9990 chunk 279 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 111 optimal weight: 0.0870 chunk 176 optimal weight: 4.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 281 HIS E 201 ASN E 361 HIS F 784 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27509 Z= 0.216 Angle : 0.666 12.166 37224 Z= 0.323 Chirality : 0.044 0.272 4280 Planarity : 0.005 0.094 4856 Dihedral : 10.600 161.593 4068 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.41 % Favored : 88.38 % Rotamer: Outliers : 4.65 % Allowed : 18.76 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.14), residues: 3452 helix: -0.82 (0.13), residues: 1504 sheet: -2.31 (0.27), residues: 288 loop : -2.67 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 545 HIS 0.004 0.001 HIS E 361 PHE 0.019 0.002 PHE A 605 TYR 0.016 0.001 TYR F 338 ARG 0.007 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 262 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8719 (tt) REVERT: A 397 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: B 201 ASN cc_start: 0.9490 (OUTLIER) cc_final: 0.9227 (p0) REVERT: B 241 ASP cc_start: 0.7906 (t0) cc_final: 0.7639 (t0) REVERT: B 327 ASP cc_start: 0.8118 (t0) cc_final: 0.7660 (t0) REVERT: B 331 GLU cc_start: 0.8771 (pp20) cc_final: 0.8488 (pp20) REVERT: B 387 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7245 (mm) REVERT: B 442 LEU cc_start: 0.4791 (OUTLIER) cc_final: 0.3975 (tt) REVERT: B 663 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.6963 (mm-40) REVERT: C 713 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8440 (p0) REVERT: C 818 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8498 (mt0) REVERT: D 312 VAL cc_start: 0.9172 (t) cc_final: 0.8934 (p) REVERT: D 798 PHE cc_start: 0.8705 (m-80) cc_final: 0.8486 (m-80) REVERT: E 615 GLU cc_start: 0.8048 (tp30) cc_final: 0.7653 (tp30) REVERT: E 687 ASP cc_start: 0.7614 (t0) cc_final: 0.7247 (t0) REVERT: E 697 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: E 783 LEU cc_start: 0.7611 (mp) cc_final: 0.6985 (tt) REVERT: E 822 MET cc_start: 0.7056 (tpp) cc_final: 0.6674 (tpp) REVERT: F 215 ILE cc_start: 0.9271 (mt) cc_final: 0.9008 (mm) REVERT: F 330 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6582 (pp) REVERT: F 336 GLN cc_start: 0.8070 (pm20) cc_final: 0.7637 (pp30) REVERT: F 669 ARG cc_start: 0.8135 (ttt180) cc_final: 0.6813 (ttm110) REVERT: F 739 PHE cc_start: 0.7214 (m-80) cc_final: 0.6603 (m-10) outliers start: 129 outliers final: 89 residues processed: 351 average time/residue: 0.3678 time to fit residues: 208.0336 Evaluate side-chains 340 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 241 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 604 MET Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 829 HIS Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 663 GLN Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 635 ASP Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain C residue 818 GLN Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 697 ASP Chi-restraints excluded: chain E residue 710 ASP Chi-restraints excluded: chain E residue 732 LEU Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 843 ASP Chi-restraints excluded: chain F residue 304 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 564 MET Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 743 PHE Chi-restraints excluded: chain F residue 793 LEU Chi-restraints excluded: chain F residue 829 HIS Chi-restraints excluded: chain F residue 843 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 0.0980 chunk 37 optimal weight: 0.2980 chunk 191 optimal weight: 0.0030 chunk 245 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 283 optimal weight: 20.0000 chunk 188 optimal weight: 3.9990 chunk 335 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 204 optimal weight: 0.8980 chunk 154 optimal weight: 0.0870 overall best weight: 0.2768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 281 HIS B 361 HIS C 335 GLN E 201 ASN F 784 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 27509 Z= 0.147 Angle : 0.637 16.662 37224 Z= 0.307 Chirality : 0.043 0.276 4280 Planarity : 0.005 0.087 4856 Dihedral : 10.050 162.674 4068 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.05 % Favored : 89.77 % Rotamer: Outliers : 3.38 % Allowed : 20.13 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.14), residues: 3452 helix: -0.67 (0.14), residues: 1499 sheet: -1.77 (0.30), residues: 259 loop : -2.51 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 792 HIS 0.002 0.000 HIS A 323 PHE 0.015 0.001 PHE D 386 TYR 0.015 0.001 TYR F 320 ARG 0.006 0.000 ARG F 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 302 time to evaluate : 3.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8638 (tt) REVERT: A 397 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: B 201 ASN cc_start: 0.9409 (OUTLIER) cc_final: 0.9134 (p0) REVERT: B 241 ASP cc_start: 0.7817 (t0) cc_final: 0.7598 (t0) REVERT: B 327 ASP cc_start: 0.8035 (t0) cc_final: 0.7569 (t0) REVERT: B 331 GLU cc_start: 0.8676 (pp20) cc_final: 0.8466 (pp20) REVERT: B 387 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6965 (mm) REVERT: B 442 LEU cc_start: 0.4611 (OUTLIER) cc_final: 0.4072 (tt) REVERT: B 537 ASP cc_start: 0.7792 (m-30) cc_final: 0.7481 (m-30) REVERT: B 663 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.6682 (mm-40) REVERT: C 562 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8691 (mm) REVERT: C 710 ASP cc_start: 0.7680 (m-30) cc_final: 0.7375 (m-30) REVERT: D 259 LEU cc_start: 0.9251 (tp) cc_final: 0.8996 (tp) REVERT: D 279 GLU cc_start: 0.8040 (pp20) cc_final: 0.7751 (pp20) REVERT: D 312 VAL cc_start: 0.9094 (t) cc_final: 0.8884 (p) REVERT: D 407 ASP cc_start: 0.8145 (t70) cc_final: 0.7860 (t0) REVERT: D 798 PHE cc_start: 0.8572 (m-80) cc_final: 0.8351 (m-80) REVERT: E 615 GLU cc_start: 0.7982 (tp30) cc_final: 0.7670 (tp30) REVERT: E 696 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7557 (pp) REVERT: E 697 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: E 783 LEU cc_start: 0.7523 (mp) cc_final: 0.6854 (tt) REVERT: E 822 MET cc_start: 0.6995 (tpp) cc_final: 0.6669 (tpp) REVERT: E 823 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6684 (mm) REVERT: F 215 ILE cc_start: 0.9227 (mt) cc_final: 0.8980 (mm) REVERT: F 217 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8432 (mm-30) REVERT: F 330 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6534 (pp) REVERT: F 336 GLN cc_start: 0.7945 (pm20) cc_final: 0.7566 (pp30) REVERT: F 669 ARG cc_start: 0.8153 (ttt180) cc_final: 0.6838 (ttm110) REVERT: F 739 PHE cc_start: 0.7096 (m-80) cc_final: 0.6525 (m-10) outliers start: 94 outliers final: 52 residues processed: 367 average time/residue: 0.3554 time to fit residues: 213.8179 Evaluate side-chains 313 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 250 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 663 GLN Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 697 ASP Chi-restraints excluded: chain E residue 710 ASP Chi-restraints excluded: chain E residue 732 LEU Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 823 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 564 MET Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 743 PHE Chi-restraints excluded: chain F residue 784 GLN Chi-restraints excluded: chain F residue 793 LEU Chi-restraints excluded: chain F residue 829 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 101 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 228 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 685 HIS E 201 ASN E 685 HIS ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 784 GLN ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27509 Z= 0.193 Angle : 0.657 14.878 37224 Z= 0.315 Chirality : 0.044 0.266 4280 Planarity : 0.005 0.088 4856 Dihedral : 10.056 162.998 4068 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.23 % Favored : 89.60 % Rotamer: Outliers : 3.31 % Allowed : 20.45 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.14), residues: 3452 helix: -0.56 (0.14), residues: 1506 sheet: -1.80 (0.29), residues: 264 loop : -2.45 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 545 HIS 0.002 0.001 HIS D 829 PHE 0.025 0.001 PHE D 386 TYR 0.020 0.001 TYR E 320 ARG 0.006 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 262 time to evaluate : 3.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8683 (tt) REVERT: A 397 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: B 201 ASN cc_start: 0.9435 (OUTLIER) cc_final: 0.9128 (p0) REVERT: B 241 ASP cc_start: 0.7880 (t0) cc_final: 0.7646 (t0) REVERT: B 327 ASP cc_start: 0.8122 (t0) cc_final: 0.7681 (t0) REVERT: B 331 GLU cc_start: 0.8760 (pp20) cc_final: 0.8511 (pp20) REVERT: B 387 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7080 (mm) REVERT: B 442 LEU cc_start: 0.4522 (OUTLIER) cc_final: 0.3855 (tt) REVERT: B 537 ASP cc_start: 0.7761 (m-30) cc_final: 0.7449 (m-30) REVERT: C 710 ASP cc_start: 0.7737 (m-30) cc_final: 0.7446 (m-30) REVERT: C 779 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8498 (mtm-85) REVERT: D 259 LEU cc_start: 0.9321 (tp) cc_final: 0.9036 (tp) REVERT: D 279 GLU cc_start: 0.8106 (pp20) cc_final: 0.7805 (pp20) REVERT: D 312 VAL cc_start: 0.9123 (t) cc_final: 0.8917 (p) REVERT: D 407 ASP cc_start: 0.8169 (t70) cc_final: 0.7872 (t0) REVERT: D 798 PHE cc_start: 0.8668 (m-80) cc_final: 0.8452 (m-80) REVERT: E 615 GLU cc_start: 0.8003 (tp30) cc_final: 0.7646 (tp30) REVERT: E 687 ASP cc_start: 0.7355 (m-30) cc_final: 0.6913 (t0) REVERT: E 696 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7591 (pp) REVERT: E 697 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: E 783 LEU cc_start: 0.7589 (mp) cc_final: 0.6934 (tt) REVERT: E 822 MET cc_start: 0.7173 (tpp) cc_final: 0.6844 (tpp) REVERT: F 215 ILE cc_start: 0.9273 (mt) cc_final: 0.9029 (mm) REVERT: F 330 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6539 (pp) REVERT: F 336 GLN cc_start: 0.7990 (pm20) cc_final: 0.7516 (pp30) REVERT: F 669 ARG cc_start: 0.8198 (ttt180) cc_final: 0.6826 (ttm110) REVERT: F 739 PHE cc_start: 0.7148 (m-80) cc_final: 0.6610 (m-10) REVERT: F 845 LEU cc_start: 0.7165 (mt) cc_final: 0.6841 (mt) outliers start: 92 outliers final: 68 residues processed: 326 average time/residue: 0.3811 time to fit residues: 200.9288 Evaluate side-chains 331 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 254 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 HIS Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 635 ASP Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 697 ASP Chi-restraints excluded: chain E residue 710 ASP Chi-restraints excluded: chain E residue 732 LEU Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 564 MET Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 743 PHE Chi-restraints excluded: chain F residue 793 LEU Chi-restraints excluded: chain F residue 829 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 9.9990 chunk 321 optimal weight: 0.7980 chunk 293 optimal weight: 6.9990 chunk 312 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 245 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 295 optimal weight: 20.0000 chunk 311 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 201 ASN ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 784 GLN ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 27509 Z= 0.197 Angle : 0.664 13.838 37224 Z= 0.318 Chirality : 0.045 0.676 4280 Planarity : 0.005 0.088 4856 Dihedral : 9.945 161.913 4068 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.78 % Favored : 89.08 % Rotamer: Outliers : 3.78 % Allowed : 20.38 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.14), residues: 3452 helix: -0.47 (0.14), residues: 1505 sheet: -1.73 (0.29), residues: 271 loop : -2.40 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 545 HIS 0.003 0.001 HIS D 829 PHE 0.027 0.001 PHE D 386 TYR 0.018 0.001 TYR E 320 ARG 0.008 0.000 ARG E 563 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 257 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8673 (tt) REVERT: A 397 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: B 201 ASN cc_start: 0.9429 (OUTLIER) cc_final: 0.9144 (p0) REVERT: B 241 ASP cc_start: 0.7915 (t0) cc_final: 0.7661 (t0) REVERT: B 327 ASP cc_start: 0.8114 (t0) cc_final: 0.7678 (t0) REVERT: B 331 GLU cc_start: 0.8776 (pp20) cc_final: 0.8502 (pp20) REVERT: B 387 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7165 (mm) REVERT: B 442 LEU cc_start: 0.4585 (OUTLIER) cc_final: 0.3870 (tt) REVERT: B 537 ASP cc_start: 0.7752 (m-30) cc_final: 0.7465 (m-30) REVERT: B 663 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.6759 (mm-40) REVERT: C 710 ASP cc_start: 0.7775 (m-30) cc_final: 0.7551 (m-30) REVERT: C 779 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8579 (mtm-85) REVERT: D 259 LEU cc_start: 0.9343 (tp) cc_final: 0.9046 (tp) REVERT: D 312 VAL cc_start: 0.9173 (t) cc_final: 0.8965 (p) REVERT: D 407 ASP cc_start: 0.8096 (t70) cc_final: 0.7833 (t0) REVERT: D 798 PHE cc_start: 0.8700 (m-80) cc_final: 0.8481 (m-80) REVERT: E 377 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8305 (mm) REVERT: E 615 GLU cc_start: 0.8054 (tp30) cc_final: 0.7643 (tp30) REVERT: E 696 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7607 (pp) REVERT: E 697 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: E 783 LEU cc_start: 0.7590 (mp) cc_final: 0.6915 (tt) REVERT: E 822 MET cc_start: 0.7191 (tpp) cc_final: 0.6852 (tpp) REVERT: F 217 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8427 (mm-30) REVERT: F 330 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6532 (pp) REVERT: F 336 GLN cc_start: 0.7977 (pm20) cc_final: 0.7478 (pp30) REVERT: F 669 ARG cc_start: 0.8107 (ttt180) cc_final: 0.6827 (ttm110) REVERT: F 673 TYR cc_start: 0.6629 (t80) cc_final: 0.6177 (t80) REVERT: F 845 LEU cc_start: 0.7077 (mt) cc_final: 0.6773 (mt) outliers start: 105 outliers final: 82 residues processed: 330 average time/residue: 0.3946 time to fit residues: 214.1721 Evaluate side-chains 338 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 245 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 HIS Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 663 GLN Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 299 MET Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 635 ASP Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 697 ASP Chi-restraints excluded: chain E residue 710 ASP Chi-restraints excluded: chain E residue 732 LEU Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 564 MET Chi-restraints excluded: chain F residue 603 PHE Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 635 ASP Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 743 PHE Chi-restraints excluded: chain F residue 784 GLN Chi-restraints excluded: chain F residue 793 LEU Chi-restraints excluded: chain F residue 823 LEU Chi-restraints excluded: chain F residue 829 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 5.9990 chunk 330 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 346 optimal weight: 10.0000 chunk 319 optimal weight: 0.0050 chunk 276 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 784 GLN ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 27509 Z= 0.161 Angle : 0.658 13.550 37224 Z= 0.313 Chirality : 0.044 0.623 4280 Planarity : 0.004 0.087 4856 Dihedral : 9.732 160.292 4068 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.37 % Favored : 89.48 % Rotamer: Outliers : 3.24 % Allowed : 20.99 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.14), residues: 3452 helix: -0.40 (0.14), residues: 1497 sheet: -1.55 (0.30), residues: 266 loop : -2.34 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 545 HIS 0.003 0.000 HIS B 685 PHE 0.036 0.001 PHE F 739 TYR 0.017 0.001 TYR E 320 ARG 0.007 0.000 ARG D 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 258 time to evaluate : 3.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8657 (tt) REVERT: A 397 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: B 201 ASN cc_start: 0.9403 (OUTLIER) cc_final: 0.9110 (p0) REVERT: B 241 ASP cc_start: 0.7900 (t0) cc_final: 0.7605 (t0) REVERT: B 327 ASP cc_start: 0.8108 (t0) cc_final: 0.7677 (t0) REVERT: B 331 GLU cc_start: 0.8709 (pp20) cc_final: 0.8468 (pp20) REVERT: B 387 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7053 (mm) REVERT: B 663 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.6703 (mm-40) REVERT: C 710 ASP cc_start: 0.7762 (m-30) cc_final: 0.7529 (m-30) REVERT: C 779 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8576 (mtm-85) REVERT: D 259 LEU cc_start: 0.9302 (tp) cc_final: 0.9029 (tp) REVERT: D 279 GLU cc_start: 0.8108 (pp20) cc_final: 0.7785 (pp20) REVERT: D 312 VAL cc_start: 0.9107 (t) cc_final: 0.8883 (p) REVERT: D 407 ASP cc_start: 0.8150 (t70) cc_final: 0.7843 (t0) REVERT: D 798 PHE cc_start: 0.8688 (m-80) cc_final: 0.8458 (m-80) REVERT: E 615 GLU cc_start: 0.8030 (tp30) cc_final: 0.7634 (tp30) REVERT: E 696 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7569 (pp) REVERT: E 697 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7595 (m-30) REVERT: E 783 LEU cc_start: 0.7525 (mp) cc_final: 0.6847 (tt) REVERT: E 822 MET cc_start: 0.7142 (tpp) cc_final: 0.6779 (tpp) REVERT: E 823 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6673 (mm) REVERT: F 217 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8460 (mm-30) REVERT: F 330 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6512 (pp) REVERT: F 336 GLN cc_start: 0.7992 (pm20) cc_final: 0.7498 (pp30) REVERT: F 590 ARG cc_start: 0.6843 (tpt-90) cc_final: 0.6449 (mmp80) REVERT: F 669 ARG cc_start: 0.8074 (ttt180) cc_final: 0.6802 (ttm110) REVERT: F 673 TYR cc_start: 0.6628 (t80) cc_final: 0.6191 (t80) REVERT: F 845 LEU cc_start: 0.6915 (mt) cc_final: 0.6609 (mt) outliers start: 90 outliers final: 71 residues processed: 320 average time/residue: 0.3567 time to fit residues: 185.1545 Evaluate side-chains 331 residues out of total 2840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 250 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 713 ASN Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 HIS Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 663 GLN Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 554 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain C residue 833 THR Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 692 LEU Chi-restraints excluded: chain D residue 716 LEU Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 781 LEU Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 361 HIS Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 530 LYS Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 697 ASP Chi-restraints excluded: chain E residue 710 ASP Chi-restraints excluded: chain E residue 732 LEU Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 823 LEU Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 564 MET Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 731 VAL Chi-restraints excluded: chain F residue 793 LEU Chi-restraints excluded: chain F residue 829 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 0.9980 chunk 294 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 254 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 276 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 283 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 784 GLN ** F 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.120573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.093970 restraints weight = 65959.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.092871 restraints weight = 42080.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094346 restraints weight = 32906.712| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 27509 Z= 0.181 Angle : 0.662 14.277 37224 Z= 0.313 Chirality : 0.045 0.638 4280 Planarity : 0.004 0.088 4856 Dihedral : 9.635 157.376 4068 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.78 % Favored : 89.08 % Rotamer: Outliers : 3.42 % Allowed : 21.07 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.14), residues: 3452 helix: -0.32 (0.14), residues: 1497 sheet: -1.64 (0.30), residues: 263 loop : -2.31 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 545 HIS 0.002 0.001 HIS D 829 PHE 0.043 0.001 PHE D 386 TYR 0.017 0.001 TYR E 320 ARG 0.007 0.000 ARG F 791 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5311.12 seconds wall clock time: 97 minutes 3.03 seconds (5823.03 seconds total)